| |
Artificial Tumor Samples
|
---|
| |
Low Frequency Variants (n = 22) VAF: 0.02 – 0.26
|
Intermediate Frequency Variants (n = 25) VAF: 0.5 – 0.86
|
High Frequency Variants (n = 25) VAF: 0.97 – 1
|
---|
MuTect
|
Somatic Candidates
|
22
|
25
|
25
|
TP
|
19
|
25
|
25
|
FN
|
0
|
0
|
0
|
FP
|
3
|
0
|
0
|
PPV
|
19/22
|
25/25
|
25/25
|
FDR
|
3/22
|
0/25
|
0/25
|
GATK-LODN
|
Somatic Candidates
|
27
|
32
|
33
|
TP
|
17
|
23
|
23
|
FN
|
5
|
5
|
2
|
FP
|
5
|
7
|
8
|
PPV
|
17/22
|
23/30
|
23/31
|
FDR
|
5/22
|
7/30
|
8/31
|
-
TP True positives, FN False negatives, FP False positives, PPV Positive Predictive Value (#TP / #FP + #TP), FDR False Discovery Rate (#FP / #FP + #TP), VAF Variant Allelic Frequency
- GATK results were not reported in the table since it detected more than 2200 candidates out of 22 or 25 TPs